BioC 3.3: CHECK report for gCMAP on linux2.bioconductor.org

Package: gCMAP

Version: 1.15.0

Command: /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings gCMAP_1.15.0.tar.gz

StartedAt: 2015-10-27 04:01:19 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 04:04:29 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 190.5 seconds

RetCode: 0

Status:  OK

CheckDir: gCMAP.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings gCMAP_1.15.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/gCMAP.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gCMAP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gCMAP’ version ‘1.15.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘bigmemoryExtras’
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘gCMAP’ can be installed ... [20s/20s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘GO.db’ ‘KEGG.db’ ‘bigmemoryExtras’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
camera_score,eSet-CMAPCollection: no visible global function definition
  for ‘camera’
induceCMAPCollection,eSet : <anonymous>: no visible global function
  definition for ‘mwhich’
mroast_score,eSet-CMAPCollection: no visible global function definition
  for ‘mroast’
romer_score,eSet-CMAPCollection: no visible global function definition
  for ‘romer’
Undefined global functions or variables:
  camera mroast mwhich romer
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [52s/33s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
mgsa_score-methods  20.577  0.214   5.851
romer_score-methods  9.214  0.387   8.810
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [36s/28s]
 [36s/29s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.3-bioc/meat/gCMAP.Rcheck/00check.log’
for details.

* installing *source* package ‘gCMAP’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (gCMAP)

name	user	system	elapsed
CMAPCollection-class	0.830	0.151	0.748
CMAPResults-class	2.417	0.017	2.433
KEGG2cmap	0.001	0.000	0.001
SignedGeneSet-class	0.055	0.000	0.055
annotate_eset_list	0.109	0.003	0.113
camera_score-methods	0.301	0.040	0.665
center_eSet	0.02	0.00	0.02
connectivity_score-methods	1.117	0.426	0.542
eSetOnDisk	0.003	0.000	0.003
eset_instances	0.05	0.00	0.05
featureScores-methods	0.277	0.135	0.411
fisher_score-methods	0.805	0.280	0.485
gCMAPData-dataset	0.264	0.100	0.353
geneIndex-methods	0.453	0.133	0.362
generate_gCMAP_NChannelSet	0.112	0.012	0.124
gsealm_jg_score-methods	0.856	0.245	0.517
gsealm_score-methods	1.842	0.125	1.983
induceCMAPCollection-methods	0.502	0.136	0.395
mapNmerge	0.001	0.000	0.001
memorize	0.003	0.000	0.003
mergeCMAPs	0.062	0.004	0.066
mgsa_score-methods	20.577	0.214	5.851
minSetSize-methods	0.703	0.256	0.530
mroast_score-methods	0.952	0.171	1.088
romer_score-methods	9.214	0.387	8.810
signedRankSumTest	0.002	0.000	0.003
splitPerturbations	0.078	0.012	0.090
wilcox_score-methods	0.986	0.484	0.683